tbuckley/cabot-search huggingface dataset:
PATH-08. A COMPREHENSIVE GENOMIC STUDY OF 390 H3F3A-MUTANT PEDIATRIC-TYPE DIFFUSE HIGH-GRADE GLIOMAS WHO CNS GRADE 4
Authors: Erik Williams, Priscilla Brastianos, Hiroaki Wakimoto, Sandro Santagata, Daniel Cahill, Tareq Juratli
Journal: Neuro-Oncology (2022)

Abstract OBJECTIVES Histone gene mutant malignant gliomas - H3K27-altered diffuse midline glioma (DMG) and diffuse hemispheric glioma (DHG) H3G34-mutant - occur in all age groups and can have significant variation in clinical outcomes. Here, we report comprehensive genomic profiling from one of the largest collections of H3F3A-mutant gliomas analyzed to date, identifying subsets defined by recurrently co-mutated genes. METHODS We identified 390 H3F3A-mutant diffuse gliomas WHO grade 4 (201 females and 189 males) that were profiled in the comprehensive genomic profiling program at Foundation Medicine between 2013-2020. Information from pathology reports, histopathology reviews, and clinical data was assessed. RESULTS Our cohort comprised 304 (77.9%) H3K27M-mutant DMG WHO grade 4 (156 females and 148 males) and 86 H3G34-mutant DHG (45 females and 41 males) with a median age of 20 years (1-74 years). H3K27M-mutant DMG distributed equally between pediatric and adult patients, with 52% of the patients older than 20 years, 30% older than 30 years, and 18% older than 40 years at the time of first diagnosis. Clonal FGFR1 hotspot mutations were exclusively detected in K27M-mutant DMG (n = 64/304, 21%; p=0.0001), with a significant association with a higher age at first diagnosis (median 32.5 years), and with a wide tumor distribution across the diencephalon. Additional genes which were significantly more frequently altered in K27M-mutant compared to G34-mutant diffuse gliomas included NF1 (31% vs. 8.1%; p=0.0001) and PIK3CA/PIK3R1 (27.9% vs. 15.1%; p=0.016). Conversely, targetable alterations of the cell-cycle pathway (CDK4/6 amplifications and CDKN2A/B deletions) were enriched in H3G34-mutant DHG (26%) compared to H3K27M-mutant DMG (7%). Potentially targetable PDGFR alterations were present in 32.5% of H3G34-mutant DHG and in 18% of H3K27M-mutant DMG. CONCLUSIONS These data expand our understanding of the tumor-specific molecular features of pediatric-type high-grade gliomas, identifying cohort sub-structure by recurrent co-mutations, which can inform diagnosis and clinical trial design.
QOL-21. REAL-WORLD QUALITY-OF-LIFE AND HEALTH UTILITIES FOR PATIENTS WITH CNS CANCERS ON THE XCELSIOR PLATFORM
Authors: Alanis Sabates, Alayna Wood, Hope Lee, Andrew Swain, Sabrina Irizarry, Chezney Hinton, Sarah Ginn, Zac Cole, Gordon Chavez, Kristina Tadic, Don Chuyka, Bryan Federowicz, Christina Proescholdt, Mark Shapiro
Journal: Neuro-Oncology (2022)

Abstract OBJECTIVE xCures operates a direct-to-patient, real-world evidence platform according to the nationwide observational research protocol XCELSIOR (NCT03793088), which aggregates medical data in an FDA-compliant electronic database. There is a relative scarcity of published results on real-world Quality-of-Life (QoL) outcomes and resulting health state utilities for patients with Central Nervous System (CNS) cancers. We sought to use the xCures platform to help address this issue. METHODS XCELSIOR participants were invited weekly to complete the EuroQol 5-Dimension (EQ-5D-5L) QoL survey. A EuroQol-endorsed model was used to estimate health state utilities from patient surveys. Survey results, utility estimates, and clinical information were analyzed to understand the influence of common mutations in glioma on patient reported outcomes. RESULTS 30 patients (21 glioblastoma, 4 oligodendroglioma, 2 diffuse midline glioma, 2 diffuse astrocytoma, 1 Schwannoma) completed at least one EQ-5D-5L survey over the course of 9 weeks. Health state utilities were positively correlated (p&amp;lt; .03) with Karnofsky Performance Score (KPS). The average utility for EGFR-mutated patients (N=6) was .578 (SD=.334) while for EGFR-wildtype patients (N=7) it was .747 (SD=.227). The average utility for MGMT-methylated patients (N=13) was .816 (SD=.139) while for non-methylated patients (N=10) it was .583 (SD=.379). The average utility for IDH-mutated patients (N=9) was .789 (SD=.153) while for non-mutated patients (N=17) it was .685 (SD=.324). The average utility for patients with a 1p/19q co-deletion (N=4) was .837 (SD=.126) while for those without a co-deletion (N=8) it was .744 (SD=.244). CONCLUSION The xCures platform has enabled the study of real-world QoL outcomes for patients with CNS cancers. This is the first report studying the influence of genetic mutations on QoL collected through patient reported outcomes. Future research aims to perform similar studies with larger number of patients.
EXTH-23. BICISTRONIC CAR-T CELLS TARGETING EGFR AND IL13RΑ2 MITIGATE ANTIGENIC HETEROGENEITY IN GLIOMA
Authors: Nannan Li, Yibo Yin, Jesse Rodriguez, Meghan Logun, Logan Zhan, Jiasi Zhang, Zev A Binder, Zhiguo Lin
Journal: Neuro-Oncology (2022)

Abstract Chimeric antigen receptor (CAR)-T cells have had a significant effect in hematological diseases, with a recent study confirming that the cells can last for ten years in vivo. Unfortunately, to date, CAR-T cells have had little effect in solid tumors. One cause of the treatment difficulty is antigenic heterogeneity. Our experience with CAR-T cells in glioblastoma suggests that addressing antigenic heterogeneity may improve the clinical efficacy. Targeting the epidermal growth factor receptor (EGFR) and interleukin 13 receptor subunit alpha 2 (IL13Rα2) individually could lead to tumor control in the short term, but it will be marked by tumor recurrence through antigen loss or downregulation in the long term. This resistance mechanism can be inhibited by combinatorial targeting. To this end, we have designed a bicistronic construct that targets both EGFR and IL13Rα2 simultaneously, to decrease the potential of antigen escape and tumor recurrence. The bicistronic CAR-T cells employ an “OR” logic gate to modify the T cells and kill the tumor cells in vitro and in vivo, in order to retain effectiveness when one target antigen is lost but the second is still present. Our experimental results demonstrate that and validate the safety and possibility of clinical translation. In addition, the efficiency of transfecting T cells with the single bicistronic vector was higher than two single vectors on monovalent CARs. In summary, the bicistronic CAR-T structure is a promising strategy to address the clinical problem of targeting antigenic heterogeneity in solid tumors and potentially level the barriers for targeted T-cell therapy. Educational Objectives: After completion, participants will be able to explain the importance of antigenic heterogeneity in solid tumors in the context of tumor escape. Participants will also be able to identify a strategy to reducing the problem of antigen escape and tumor recurrence through the implementation of bicistronic CARs.
TMIC-37. SINGLE-CELL CHARACTERIZATION OF THE IMMUNE LANDSCAPE OF EXTREME LONG-TERM SURVIVORS WITH MALIGNANT GLIOMA
Authors: Brecht Decraene, Asier Antoranz, Tatjana Verbeke, Maxime Vanmechelen, Pouya Nazari, Lien Solie, Nikolina Dubroja, Marleen Derweduwe, Lien Spans, Isabelle Vanden Bempt, Raf Sciot, Frederik De Smet, Steven De Vleeschouwer
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond two years despite extensive therapy, which consists of maximal safe surgical resection, radiotherapy and/or chemotherapy. Recently, it has become clear that GBM is not one homogeneous entity and that both intra-and intertumoral heterogeneity contribute significantly to differences in tumoral behavior which may consequently be responsible for differences in survival. Strikingly and despite its dismal prognosis, small fractions of GBM patients seem to display extreme extended survival compared to the large majority of patients. The underlying mechanisms for this peculiarity remain largely unknown however, even though emerging data suggest that both cancer cell-autonomous and microenvironmental factors and their interplay probably play an important role. We used high-dimensional, multiplexed immunohistochemistry to spatially, and cytometry by time-of-flight to quantitively, characterize the cell constitution and interactions within the tumor microenvironment (TME) in 21 extreme long-term survivors (living over 10 year) and 42 deeply matched controls and therefore short-term survivors (living under 1.5 year) on a single cell level. For all tumors (epi)genetic data was also collected. We identified a high level of both inter-and intrapatient heterogeneity defined by several distinct tumoral niches, as well as described interactions within these niches and with the surrounding infiltrating immune cells of the TME in GBM. Finally, by linking patient characteristics with the heterogeneous immune composition we are able to create an immune stratification that can be linked to patient survival in GBM. Therefore, this study is an essential initial step towards strategies to alter the TME in a favorable way with a personalized modulation strategy.
EXTH-43. XPO1 INHIBITOR SELINEXOR SENSITIVITY IN GLIOBLASTOMA: POTENTIAL ROLE OF MGMT ACTIVATION THROUGH PKA-CREB PATHWAY
Authors: Yuta Suzuki, Shiv Gupta, Jann Sarkaria, Gaspar Kitange
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Glioblastoma (GBM) is the most common and aggressive form of adult brain tumor and is an incurable disease due to primary and secondary resistance to therapy. We recently examined the candidate genes modulating temozolomide (TMZ) resistance using genome-wide shRNA screening in TMZ-resistant U251 (U251TMZ) model. We identified a total of 134 TMZ-resistant candidate genes, including Karyopherin A1 (KPNA1) and Exportin 1 (XPO1), the genes critical for nucleocytoplasmic (NC)-transport. Interestingly, XPO1 inhibitor Selinexor is an FDA-approved agent for refractory multiple myeloma, and there is an ongoing interest in evaluating Selinexor for GBM therapy. Therefore, we hypothesized that Selinexor is a promising drug for overcoming TMZ resistance. METHODS and RESULTS We conducted a series of experiments in vitro using Selinexor with and without TMZ. Selinexor and TMZ alone didn’t significantly block the growth of U251TMZ cells. In contrast, Selinexor significantly re-sensitized resistant U251TMZ cells to TMZ. Interestingly, MGMT-methylated GBM39 cells were sensitive to Selinexor alone, TMZ alone, and to combined Selinexor/TMZ treatment. Contrarily, MGMT-unmethylated GBM43 cells were only sensitive to combined Selinexor/TMZ treatment. These findings suggested that similar to TMZ, Selinexor sensitivity may be influenced by MGMT expression status, with MGMT expressing cells showing resistance. In line with this notion, re-expression of exogeneous MGMT blocked sensitivity of MGMT-methylated U251 cells to Selinexor and TMZ, but such inhibition was not observed in U251 expressing vector alone. Interestingly, the concentration-dependent experiments demonstrated that Selinexor can induce MGMT expression in unmethylated T98G, GBM6, GBM14, and GBM43 cells. Selinexor-induced MGMT expression was accompanied with increased phosphorylation of CREB protein. CONCLUSION These results suggest that Selinexor sensitivity alone and with TMZ may be limited to MGMT-methylated GBM cells and may increase MGMT expression in unmethylated cells through activation of PKA-CREB pathway. Future studies will evaluate how MGMT may impact the sensitivity of GBM cells to Selinexor.
TMET-05. MAGMAS FACILITATES METABOLIC CHANGES INDUCED BY STRESSORS IN GLIOBLASTOMA
Authors: Javier Lepe, Naomi Lomeli, Chris Douglas, Kaijun Di, Daniela Bota
Journal: Neuro-Oncology (2022)

Abstract The dynamic nature of tumor microenvironments contributes to tumor heterogeneity generating subpopulations of cells that are resistant to treatment in glioblastoma (GBM). The high recurrent rate of GBM tumors in patients can partially be explained by the presence of glioma stem cells (GSCs), which are thought to give rise to resistant clones against chemotherapy. As solid tumors expand, cancer cells can disrupt the tumor microenviroment by disrupting the blood brain barrier. Pericytes and astrocytes detach from the vascular endothelial cells, forming leaky vessels, which leads to thrombosis and eventually necrosis. Necrosis is a hallmark signature of GBM, as oxygen and nutrient supply runs low which can be observed through contrast imaging. Cancer cells go through a phenotypic change by upregulating stemness genes and glycolytic metabolism. Cells migrate away from hypoxic and nutrient deprived regions forming pseudopalisading cells which are an indication of cells becoming more invasive and malignant. Mitochondrial protein trafficking is a tightly regulated mechanism which selectively allows specific peptides carrying a mitochondrial targeting sequence (MTS) to be transported through the TOM40 and TIM23 complexes. Magmas, a TIM23 subunit, negatively regulates DNAJC19 by inhibiting its stimulatory activity on Hsp70 in the mitochondrial matrix. The regulation of the ATPase activity on Hsp70 is critical for processing pre-cursor proteins through the TIM23 complex into the mitochondrial matrix. Our laboratory has uncovered a novel role of Magmas activity in GBM cells under serum starved conditions in vitro. Magmas is downregulated in serum starved cells which allows for an increase of mitochondrial matrix proteins, which include key subunits important for forming electron transport chain complexes. This influx of ETC proteins can explain how cells are able to reduce aerobic glycolysis and increase oxidative phosphorylation (OXPHOS), a mechanism that can be exploited for potential therapeutic treatment in patients with GBM.
BIOM-49. A PILOT STUDY OF CEREBROSPINAL FLUID EXOSOMAL SMALL RNA-SEQUENCING IN PEDIATRIC MEDULLOBLASTOMA PATIENTS ON THE NEXT CONSORTIUM “HEAD START” 4 PROTOCOL
Authors: Erica Bell, Amy Webb, Joseph Stanek, Megan Blue, Parth Patel, Diana Thomas, Christopher Pierson, Nikol Mladkova, Jessica Fleming, Katherine Miller, Olivia Grischow, Thomas Liszkay, Randall Olshefski, Susan Chi, Melanie Comito, Gregory Friedman, Anne Bendel, Scott Coven, Caroline Hastings, Elias Sayour, James Garvin, Tom Davidson, Albert Cornelius, Christopher Moertel, Claire Mazewski, Andrew Walter, Robert Greiner, Diane Puccetti, Hamza Gorsi, Kathleen Dorris, Ziad Khatib, Arnab Chakravarti, Catherine Cottrell, Shahab Asgharzadeh, Annie Huang, Rod Rassekh, David Limbrick, Daniel Boue, Jaclyn Biegel, Elaine Mardis, Girish Dhall, Jonathan Finlay, Jeffrey Leonard
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Head Start 4 is a randomized clinical trial to determine whether dose-intensive tandem consolidation, compared with a single cycle, with autologous hematopoietic progenitor cell rescue provides a survival benefit in pediatric patients with medulloblastoma or other embryonal tumors. The trial incorporates upfront molecular subgrouping and non-mandatory, prospective blood and cerebrospinal fluid (CSF) collection. This pilot study aimed to identify exosomal non-coding RNAs (exo-ncRNAs) that might serve as novel diagnostic and/or treatment response biomarkers. METHODS CSF(1-2mLs) from 11 controls (non-tumor) and 27 medulloblastoma participants including 23 obtained at baseline, 22 at the end of induction, 3 post-consolidation, and 4 relapse time points, were profiled. Exosome isolation and small RNA-sequencing were performed by System Biosciences. Differential gene expression (DGE) was performed in R (DESeq2). Variations in gene expression profiles between samples were visualized using principal component analysis. RESULTS After limiting to ncRNAs with expression of 2 counts per million in 50% or more of the samples in each comparison, ~9,500 ncRNAs were detected. DGE analyses revealed 118 ncRNAs with log2 fold change(FC) &amp;gt;2 and 1 ncRNA with log2FC&amp;lt; -2 in baseline CSF samples compared to controls. In contrast, 11 ncRNAs(log2FC &amp;gt;2) and 1 ncRNA(log2FC&amp;lt; -2) were detected in end of induction CSF samples compared to controls. Comparing end of induction to baseline CSF samples accounting for paired samples, 0 ncRNAs(log2FC &amp;gt;2) and 52 ncRNAs(log2FC&amp;lt; -2) were detected. CONCLUSIONS Overall, our data indicate that exosomal small RNA-sequencing of limited CSF volumes is feasible. Differential expression and distinct clustering between tumor baseline samples compared to non-tumor controls was observed. CSF-derived exo-ncRNAs at end of induction also demonstrated “normalization” of ncRNA profiles, signifying CSF biomarkers may serve a role in diagnosis and molecular response assessment. A comprehensive analysis including multi-marker predictive model development and molecular subgrouping will be undertaken at completion of study enrollment.
TMET-24. MITOCHONDRIAL AND GENE EXPRESSION CHANGES IN BRAIN TUMOR CELLS GROWN IN Β-HYDROXYBUTYRATE
Authors: Ahmad Kareem Almekkawi, Rachelle Sheets, Brianna Werner, Richard Perryman, Indrapal Singh, Mohammad Karim, Richard Frye, Nelofer Syed, Adrienne Scheck
Journal: Neuro-Oncology (2022)

Abstract Malignant brain tumors are devastating diseases with poor outcomes. The search for more effective therapeutic combinations has led to investigation of the use of a therapeutic ketogenic diet (KD) as an adjuvant therapy based on the metabolic dysregulation that is a hallmark of cancer. KD sometimes results in extended survival, but like all cancer therapies the tumor eventually becomes resistant. Resistance can arise due to the “metabolic remodeling” of resistant cells due to limitations in nutrient availability and other signals from the tumor microenvironment. We are investigating the molecular and mitochondrial changes of tumor cells grown in β-hydroxybutyrate (BHB), the main ketone produced when following a therapeutic KD, to partially recapitulate the long-term effects of the KD on patients. Murine malignant glioma cells (GL261-luc2) were cultured long term in 2, 5 or 10mM BHB. The Agilent XFe96 Seahorse Analyzer was used to measure changes in cell metabolism. Epigenetic changes that occur in the mitochondria were interrogated using DNA methylation assays. Finally, we implanted BHB resistant glioma cells intracranially in mice and carried out RNAseq to determine the mechanisms by which these cells adapt. Seahorse analyses of GL261-luc2 cells grown in BHB demonstrated changes in several respiratory parameters including maximal respiration and reserve capacity. In addition, there is a statistically significant decrease in mitochondrial DNA methylation with increasing concentrations of BHB. RNAseq analysis of BHB resistant GL261 tumors showed changes in pathways related to mitochondrial translation and the electron transport chain. Our preliminary results show that the heterogeneity seen in these tumors is recapitulated in the various mitochondrial respiration parameters. Further, these may be altered as a consequence of BHB therapy. An understanding of the genetic and mitochondrial changes that occur when cells become resistant will lead to a more effective use of the KD as an adjuvant therapy.
NIMG-07. APPLYING A GLIOMA-TRAINED DEEP LEARNING AUTO-SEGMENTATION TOOL ON BM PRE- AND POST-RADIOSURGERY
Authors: Manpreet Kaur, Sunitha Varghese, Leon Jekel, Niklas Tillmanns, Sara Merkaj, Khaled Bousabarah, MingDe Lin, Jitendra Bhawnani, Veronica Chiang, Mariam Aboian
Journal: Neuro-Oncology (2022)

Abstract PURPOSE Stereotactic radiosurgery (SRS) has become the mainstay to treat BM. Follow-up MRI provides important information on lesion treatment response and guides future therapy planning. Volumetric measurements of BM have shown promise over traditional uni- and two-dimensional measurements in more accurate and repeatable assessment. However, routine clinical use has yet to be achieved because the workflow is laborious. In previous work, we developed a PACS-integrated deep learning algorithm for automatic high- and low-grade glioma 3D segmentation. In this work, we applied this U-Net to segment BM on pre- and post-Gamma Knife (GK) MRI and evaluated the performance. METHODS 10 pre- and post-GK studies were autosegmented in five randomly selected patients (melanoma n= 3, breast n= 2). The glioma trained algorithm segmented the “Whole Tumor” (tumor core+peritumoral edema on T2w-FLAIR) and “Tumor Core” (CE tumor core+necrosis on SPGR). The AI generated segmentation was then revised as needed by a board-certified neuroradiologist and the dice-similarity-coefficient (DSC) between the revised and automatic volumetric segmentations were calculated. RESULTS Four patients had multicentric (2-4 BM) lesions. The mean± SD DSC for Whole Tumor and Tumor Core were 0.92±0.06 and 0.46±0.30 for pretreatment, 0.84±0.09 and 0.41±0.25 for posttreatment BM, respectively. The tool detected lesions with a sensitivity of 45% (5/11) for pretreatment and 50% (3/6) for posttreatment lesions. Three pretreatment and all posttreatment lesions that were not detected by the autosegmentation tool showed a very faint hyperintense peritumoral edema in T2w-FLAIR. CONCLUSION Volumetric segmentation of edema on FLAIR using the glioma-trained segmentation algorithm on pre- and post-GK BM did not require major adjustment of segmentation if it detects the lesion. On the other hand, with low sensitivity of lesion detection and low DSC for enhancing component, dedicated training of the algorithm on annotated BM data will be needed.
NIMG-106. WHAT’S BEHIND TSPO PET LABELLING: DIGGING FOR THE HISTOLOGICAL, CELLULAR AND MOLECULAR CORRELATES
Authors: Lorraine Weidner, Julia Lorenz, Franziska Dekorsy, Stefanie Quach, Victoria Ruf, Laura Bartos, Peter Hau, Joerg-Christian Tonn, Peter Bartenstein, Louisa von Baumgarten, Matthias Brendel, Nathalie Albert, Markus Riemenschneider
Journal: Neuro-Oncology (2022)

Abstract TSPO is frequently upregulated in glioblastoma. Despite its use as an imaging biomarker for PET in glioma, the interpretation is challenging due to the heterogeneity of cell populations that could contribute to the TSPO-PET signal. We therefore dissected TSPO labelling in connection with the underlying histopathological and molecular features in biopsy samples from glioma patients. Comparing regions of high and low TSPO-PET signal in 58 patients, we assessed TSPO protein expression and expression of cell differentiation markers by use of immunohistochemistry on consecutive sections and by multiplex stains. Our results suggest that apart from microglia and macrophages the glial tumor cells relevantly contribute to the overall TSPO signal in glioma patients. To identify hallmarks and GO terms associated with TSPO labelling/expression we next performed RNAseq in 33 patients. Using DESeq2 followed by FUMA and Reactome as well as GSEA with normalized counts, we identified three TSPO-dependent functional clusters, i.e. apoptosis/DNA repair, extracellular matrix organization and immune system. On the DNA level, we analyzed the TSPO promoter by direct bisulfite sequencing suggesting that a loss of TSPO methylation may mechanistically contribute to the TSPO overexpression observed in high-grade gliomas. Exceeding our investigations on glioma biopsies we stained tissue microarrays (130 individuals) for TSPO that cover a broader spectrum of both human brain pathologies (13 different entities) and non-neoplastic tissues (14 different brain regions). We here found a high degree of heterogeneity of TSPO expression between entities and regions. Merging this information with TSPO-PETs from respective patients/brain regions allows to generate a map of TSPO expression in healthy and diseased brain for clinical use. Altogether, our approach of integrating histological, molecular and imaging data will provide unique insights into TSPO-PET enrichment patterns which may help to better understand and to comprehensively describe the clinical relevance of this novel imaging biomarker.